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// SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0
#include <seqan3/alphabet/nucleotide/dna4.hpp>
#include <seqan3/core/debug_stream.hpp>
#include <seqan3/search/fm_index/fm_index.hpp>
#include <seqan3/search/search.hpp>
using namespace seqan3::literals;
void run_text_single()
{
seqan3::dna4_vector text{
"CGCTGTCTGAAGGATGAGTGTCAGCCAGTGTAACCCGATGAGCTACCCAGTAGTCGAACTGGGCCAGACAACCCGGCGCTAATGCACTCA"_dna4};
seqan3::fm_index index{text};
seqan3::debug_stream << "===== Running on a single text =====\n"
<< "The following hits were found:\n";
for (auto && result : search("GCT"_dna4, index))
seqan3::debug_stream << result << '\n';
}
void run_text_collection()
{
std::vector<seqan3::dna4_vector> text{"CGCTGTCTGAAGGATGAGTGTCAGCCAGTGTA"_dna4,
"ACCCGATGAGCTACCCAGTAGTCGAACTG"_dna4,
"GGCCAGACAACCCGGCGCTAATGCACTCA"_dna4};
seqan3::fm_index index{text};
seqan3::debug_stream << "===== Running on a text collection =====\n"
<< "The following hits were found:\n";
for (auto && result : search("GCT"_dna4, index))
seqan3::debug_stream << result << '\n';
}
int main()
{
run_text_single();
seqan3::debug_stream << '\n';
run_text_collection();
}
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